Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States; Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
Valerie Le Sage
Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
Gabriella H Padovani
Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
Michael Calderon
Department of Cell Biology, Center for Biologic Imaging, University of Pittsburgh, Pittsburgh, United States
Center for Evolutionary Biology and Medicine, University of Pittsburgh, Pittsburgh, United States; Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, United States
Department of Microbiology & Molecular Genetics, University of Pittsburgh, Pittsburgh, United States; Center for Vaccine Research, University of Pittsburgh School of Medicine, Pittsburgh, United States
The influenza A virus (IAV) genome consists of eight negative-sense viral RNA (vRNA) segments that are selectively assembled into progeny virus particles through RNA-RNA interactions. To explore putative intersegmental RNA-RNA relationships, we quantified similarity between phylogenetic trees comprising each vRNA segment from seasonal human IAV. Intersegmental tree similarity differed between subtype and lineage. While intersegmental relationships were largely conserved over time in H3N2 viruses, they diverged in H1N1 strains isolated before and after the 2009 pandemic. Surprisingly, intersegmental relationships were not driven solely by protein sequence, suggesting that IAV evolution could also be driven by RNA-RNA interactions. Finally, we used confocal microscopy to determine that colocalization of highly coevolved vRNA segments is enriched over other assembly intermediates at the nuclear periphery during productive viral infection. This study illustrates how putative RNA interactions underlying selective assembly of IAV can be interrogated with phylogenetics.
